Method1
You need to add the following to your server side link/button:
OnClientClick="aspnetForm.target ='_blank';"My entire button code looks something like:
<asp:LinkButton ID="myButton" runat="server" Text="Click Me!" OnClick="myButton_Click" OnClientClick="aspnetForm.target ='_blank';"/>
Method 2
In the server side OnClick I do a Response.Redirect("MyPage.aspx"); and the page is opened in a new window.
The other part you need to add is to fix the form's target otherwise every link will open in a new window. To do so add the following in the header of your POPUP window.
<script type="text/javascript">
function fixform() {
if (opener.document.getElementById("aspnetForm").target != "_blank") return;
opener.document.getElementById("aspnetForm").target = "";
opener.document.getElementById("aspnetForm").action = opener.location.href;
}
</script>and
<body onload="fixform()">